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How to start folding a DeNovo (freestyle) puzzle?
from discussion on #global with itskimo and others Start by shaking wiggling side chains but do not move the backbone just yet. First define the secondary structures. These are the Sheets, Helices, Loops. Then freeze the Sheets and Helices. Next by wiggling the backbone the protein well start to bend. Start the ci= low and then slide up higher as it starts to fold together. So help it to fold at the bends by banding between the frozen sheets. Fold it up. Add more bands between the frozen sheets and also going out to the sides. These extra bands well help to anchor the protein and keep it flat. As the protein starts to fold up help it along. Try to keep it flat and from making a huge knot. Keep the sheets frozen and band between them. Now the protein starts to come together, wiggle for a while at ci= 0.05 rising the value slowly. http://fold.it/portal/files/chatimg/irc_192195_1299872358.png Usually the protein gets stuck at this point but, remember orange in blue out. Then try wiggling and getting the sheets better aligned and then Tlaloc hydro or repeat settle and others to keep things together seems to work well. Now for a helix First freeze the whole protein and then unfreeze the parts we well be working on. Also unfreeze the end loops to give the helix room to form and move. http://fold.it/portal/files/chatimg/irc_192195_1299872637.png Next build the helix by defining the secondary structure as a helix and rebuilding. http://fold.it/portal/files/chatimg/irc_192195_1299872721.png After a nice helix forms stop it. http://fold.it/portal/files/chatimg/irc_192195_1299872777.png There are lots of conflicts so do wiggles first. By using a low ci= at first and then raising the ci= value the conflicts become less. Now freeze the entire protien and unfreeze the other side for the next helix. http://fold.it/portal/files/chatimg/irc_192195_1299872948.png On this side we well have to define the structure as a heliix first. http://fold.it/portal/files/chatimg/irc_192195_1299873034.png And then rebuild to make the helix form. http://fold.it/portal/files/chatimg/irc_192195_1299873062.png After rebuilding for a while we get a good helix. This helix can be frozen to help hold its shape. http://fold.it/portal/files/chatimg/irc_192195_1299873235.png Now we try to put it all together By unfreezing most of the protien but leaving the sheets frozen to keep them flat. The helix can be frozen also to keep them streight. The loops should be unfrozen so they can flex and twist as the protein starts to settle. In the middle of te protein you can see a helix that wants to be a sheet so we well redefine it and make it so. http://fold.it/portal/files/chatimg/irc_192195_1299873372.png After you get the sheet streight freeze the new sheet and wiggle some more. http://fold.it/portal/files/chatimg/irc_192195_1299873499.png Hopefully the helix well settle into a good position. And you are on your way. http://fold.it/portal/files/chatimg/irc_192195_1299873544.png Some of the sheets are comming together better forming bonds. http://fold.it/portal/files/chatimg/irc_192195_1299873605.png Remove some bands and hope it stays together. http://fold.it/portal/files/chatimg/irc_192195_1299873778.png Wiggle shake sidechains and run something like a walker or bander script like tlaloc repeat seatle or tlaloc hydro or contract So here it is not great but it was fast. Now we need to take more time lineing up the sheets better. http://fold.it/portal/files/chatimg/irc_192195_1299874055.png http://fold.it/portal/files/chatimg/irc_192195_1299874341.png By running scripts the protein is able to compact a bit more but there are still some annoying voids. http://fold.it/portal/files/chatimg/irc_192195_1299874610.png Another with mostly sheets http://fold.it/portal/files/chatimg/irc_192195_1299874714.png http://fold.it/portal/files/chatimg/irc_192195_1299875435.png Could use some more sheet work. Once the bonds are well formed it should stabilize. Then a quick rebuild of the helices to coil them up a bit better. http://fold.it/portal/files/chatimg/irc_192195_1299875819.png Here is a way to move a helix through a frozen protien Fist freeze protien and unfrees the helix and loop that you want to move to the other side. Then band to where you want the helix to be and rebulid http://fold.it/portal/files/chatimg/irc_192195_1299879263.png http://fold.it/portal/files/chatimg/irc_192195_1299879296.png *if you drag it it well be more twisted but if you rebuild thru to the outher side the helix stayes more in the same stance http://fold.it/portal/files/chatimg/irc_192195_1299879542.png http://fold.it/portal/files/chatimg/irc_192195_1299879555.png http://fold.it/portal/files/chatimg/irc_192195_1299879573.png just a different way of doing it *or you could drag it around wiggle and band and unfreeze etc rebuild etc *Rebuild tries to go to where you have placed the bans even through stuff thats frozen to the other side and beyond *now the helix are next to each other http://fold.it/portal/files/chatimg/irc_192195_1299879877.png *Wiggle http://fold.it/portal/files/chatimg/irc_192195_1299883252.png http://fold.it/portal/files/chatimg/irc_192195_1299883325.png http://fold.it/portal/files/chatimg/irc_192195_1299883519.png *now the sheets are lined up better http://fold.it/portal/files/chatimg/irc_192195_1299884106.png *but the helix is misbehaving http://fold.it/portal/files/chatimg/irc_192195_1299884187.png *so a rebuild is in order http://fold.it/portal/files/chatimg/irc_192195_1299884330.png *There we are with 2 helix and nice flat sheets http://fold.it/portal/files/chatimg/irc_192195_1299884630.png http://fold.it/portal/files/chatimg/irc_192195_1299884721.png *Stretched them and rebuilt the sheets to pull them flat *Getting better at this http://fold.it/portal/files/chatimg/irc_192195_1299886443.png *still need to hide those yellow balls better *finaly nice sheets but that helix is gone wild http://fold.it/portal/files/chatimg/irc_192195_1299888670.png *Judecca's version http://fold.it/portal/files/chatimg/irc_9330_1299874447.png http://fold.it/portal/files/chatimg/irc_9330_1299874502.png **Started with the sheets. but locked them so they stayed straight and banded them into something that resembled a protein **if you'd look at most of my solutions. you'll find i always leave some bands on the sheets. and just enable and disable them when i need to keep things stable http://fold.it/portal/files/chatimg/irc_9330_1299876003.png **Makes it alot easier to do moves that would normally blow the protein apart. **Try leaving them enabled for a loop rebuild script.. or leave the sheets frozen a lot longer and band them (keeps the sheets flatter) **Stops them from curling or twisting up. when you choose unfreeze kinda depends on when you want a quick point jump. *Firejuggler's: http://fold.it/portal/files/chatimg/irc_62014_1299884770.png **Looked lined up well. nice bonds forming *Rav's:http://fold.it/portal/files/chatimg/irc_ *174969_1299878991.png See a video by Phallicies with cut points http://www.youtube.com/watch?v=5750OScmWpE Category:Strategy Category:Videos